If you are losing 4" of water per day, any leak around the perimeter of the liner, whether stream or pond, would, by now, have created a very saturated area of soil. You, I believe, have already checked the integrity of the Skimmer Face Plate and the Waterfall Weir Face Plate. We can rule out evaporation. The bulkhead fitting on the Biofalls is the only place left where a leak OUTSIDE of the pond's containment is possible.
If it is not here, my friend, then you have inadvertently overlooked something or you need to call the local authorities to find out if anyone has reported a herd of elephants running loose in the vicinity.